A scenario for the hobo transposable element invasion, deduced from the structure of natural populations of Drosophila melanogaster using tandem TPE repeats

Temporal surveys of hobo transposable elements in natural populations reveal a historical pattern suggesting a recent world-wide invasion of D. melanogaster by these transposons, perhaps following a recent horizontal transfer. To clarify the dynamics of hobo elements in natural populations, and thus to provide further data for our understanding of the hobo invasion, TPE tandem repeats, observed in the polymorphic S region of the element, were used as molecular markers. The number of TPE repeats was studied in 101 current populations from around the world, and in 63 strains collected in the past. This revealed a geographical distribution which seems to have been stable since the beginning of the 1960s. This distribution is compatible with a number of hypotheses for the dynamics of hobo elements. We propose a scenario based on an invasion in two stages: first, a complete invasion by elements with three TPE repeats, followed by the beginning of a new invasion involving hobo elements with five or seven repeats.     

High polymorphism of TPE repeats within natural populations of Drosophila melanogaster: a gradient of the 5TPE hobo element in Western Europe

To find out whether the polymorphism of TPE repeats of the hobo transposable element observed in some populations results from polymorphism within flies or from variability between flies, or both, we carried out isofemale line analyses of 25 populations. We found that polymorphic populations result from the presence of polymorphic flies combined with interfly variability within these populations. The fact that populations display different levels of polymorphism, i.e., different types of element and different frequencies of polymorphic flies, can be used to differentiate between qualitatively identical populations. This showed that the geographical structuring previously observed is reinforced and, in particular, that the western European populations, which have 3TPE and 5TPE elements, display a centrifugal decrease in the frequency of 5TPE hobo elements which start in western France. This gradient supports the hypothesis of a dynamic invasion by this type of elements: a total invasion by 3TPE elements, followed by further invasions involving other types of hobo elements. Moreover, the analysis of numerous sequences in current populations revealed the existence of seven types of never-previously described hobo elements with regard to TPE repeats. This diversity, which contrasts with the conservation of other parts of the element, highlights the high mutation rate of the S region.     

Behavior of the hobo transposable element with regard to TPE repeats in transgenic lines of Drosophila melanogaster

The hobo transposable element of Drosophila melanogaster is known to induce a hybrid dysgenesis syndrome. Moreover it displays a polymorphism of a microsatellite in its coding region: TPE repeats. In European populations, surveys of the distribution of hobo elements with regard to TPE repeats revealed that the 5TPE element is distributed along a frequency gradient, and it is even more frequent than the 3TPE element in Western populations. This suggests that the invasive ability of the hobo elements could be related to the number of TPE repeats they contain. To test this hypothesis we monitored the evolution of 16 lines derived from five initial independent transgenic lines bearing the 3TPE element and/or the 5TPE element. Four lines bearing 5TPE elements and four bearing 3TPE elements were used as a noncompetitive genetic background to compare the evolution of the 5TPE element to that of the 3TPE element. Eight lines bearing both elements provided a competitive genetic context to study potential interactions between these two elements. We studied genetic and molecular aspects of the first 20 generations. At the molecular level, we showed that the 5TPE element is able to spread within the genome at least as efficiently as the 3TPE element. Surprisingly, at the genetic level we found that the 5TPE element is less active than the 3TPE element, and moreover may be able to regulate the activity of the 3TPE element. Our findings suggest that the invasive potential of the 5TPE element could be due not only to its intrinsic transposition capacity but also to a regulatory potential.     

Identification of a full-size hobo element and deletion-derivatives in Korean populations of Drosophila melanogaster.

We have isolated and characterized several members of the hobo transposable element family from Korean populations of Drosophila melanogaster. All of the Korean lines tested appeared to have 3.0 kb hobo elements and a high copy number of smaller derivatives of the element. To determine whether a 3.0 kb hobo element of these populations is consistent with the role of an autonomous hobo element, we cloned and sequenced this hobo element. Based on the result of the entire DNA sequence, a cloned 3.0 kb element called HKN96, it was found to be the same as a fully-functional 2959 bp HFL1-type sequence. Each small element appeared to have arisen from the HFL1 element by a different internal deletion. A specific 1.7 kb Kh hobo element, which is the most abundant in the Korean lines tested, seems to have originated from the HFL1 hobo element by an internal deletion of 1253 bp by the removal of nucleotides between positions 939 and 2191. The sequences of the Th1 and Th2 elements appeared to be identical to that of the HFL1 with the exception of internal deletions of 1442 bp and 1455 bp removing nucleotides 940-2381 and 923-2377, respectively. Based on the number of TPE repeats, all of the members of the hobo element family in Korean lines tested have three perfect S repeats. The widespread presence of identical copies of the Kh deletion derivative suggests that it might have a role in the regulation of hobo-induced hybrid dysgenesis.     

Patterns of hobo elements and their effects in natural populations of Drosophila melanogaster in Japan

We studied the dynamics of hobo elements of Drosophila melanogaster in Japan with the goal of better understanding the invasion and evolution of transposons in natural populations. One hundred and twenty-six isofemale lines and 11 older stocks were tested for the presence and genetic phenotype of hobo elements. The oldest H strain, containing complete and deleted hobo elements, is Hikone-H (1957), but Hikone-R (1952) has no hobo-homologous sequences. The findings suggest that the hobo element invaded Japanese populations in the mid-1950s, at about the same time as the P element invasion in Japan. This chronology is consistent with the hypothesis of a recent worldwide hobo element invasion into D. melanogaster in the mid-1950s. In recently collected populations, H degrees strains (low hobo activity and high repression potency) are predominant, whereas H+ strains (high hobo activity and high repression potency) are predominant in the Sakishima Islands, the most southwestern islands of the Japanese archipelago. H' strains (high hobo activity and low repression potency) were first found in limited island populations. Japanese populations have not only full-size hobo elements and 1.5 kb Th elements but also characteristic deletion derivatives (1.6 and 1.8 kb XhoI fragments) that we have named Jh elements. These results are consistent with transgenic experiments with complete hobo elements, in which populations evolved to H+ or H degrees via H', and in which 1.8 kb fragments appeared. We conclude that hobo elements invaded the central region of Japan, spread to the far islands, and that the invasion is currently at an intermediate, nonequilibrium stage.     

Distribution of hobo transposable elements in natural populations of Drosophila melanogaster.

Forty-six strains derived from American and French natural populations of Drosophila melanogaster were tested for the presence and activity of hobo elements by using Southern blotting and a gonadal dysgenesis assay. The oldest available strains exhibited weak detectable hybridization to the hobo-element probe and revealed neither hobo-activity potential nor hobo-repression potential. In contrast, all recently collected strains harbored hobo sequences and revealed a strong hobo-repression potential but no strong hobo-activity potential. On the basis of restriction-enzyme analysis, old strains appear to have numerous fragments hybridizable to hobo sequences, several probably conserved at the same locations in the genome of the tested strain and others dispersed. In recently isolated strains, and unlike the situation in the published sequence of the cloned hobo108 element, a PvuII site is present in the great majority of full-sized hobo elements and their deletion derivatives. When the genetic and molecular characteristics are considered together, the available evidence is consistent with the hypothesis of a worldwide hobo-element invasion of D. melanogaster during the past 50 years. Comparison of data from the I-R and P-M systems suggests that the putative invasion followed the introduction of the I element but preceded that of the P element. This hypothesis poses the problem of the plausibility of three virtually simultaneous element invasions in this species. Such a possibility might be due to a modification of the genetic structure of American populations of D. melanogaster during the first part of the 20th century.     

Unraveling the evolutionary scenario of the hobo element in populations of Drosophila melanogaster and D. simulans in South America using the TPE repeats as markers

Transposable elements (TEs) are nucleotide sequences found in most studied genomes. These elements are highly diversified and have a large variation in nucleotide structure and mechanisms of transposition. hobo is a member of class II, belonging to hAT superfamily, described inDrosophila melanogaster, and it presents in its Open Reading Frame, a repetitive region encoding the amino acids threonine-proline-glutamic acid (TPE), which shows variability in the number of repeats in some regions of the world. Due to this variability some evolutionary scenarios of the hobo element are discussed, such as the scenario of the invasion of hobo element in populations ofD. melanogaster. In the present study, we investigated 22 DNA sequences of D. melanogaster and seven sequences ofD. simulans, both from South America, to check the number of repetitions of TPE, in order to clarify the evolutionary scenario of thehobo element in these populations. Our results showed a monomorphism in populations of both species in South America, with only three TPE repeats. Hence, we discuss and propose an evolutionary scenario of the invasion of the hobo element in populations of D. melanogaster and D. simulans.     

Transposition of the hobo element in Drosophila melanogaster somatic cells

Somatic mutation and recombination test on wing cells of Drosophila melanogaster showed that the recombination frequency in the somatic tissues of strains studied correlated with the presence of a full-length copy of the hobo transposable element in the genome. Transposition of hobo in somatic tissue cells at a frequency 3.5 x 10-2 per site per X chromosome was shown by fluorescence in situ hybridization with salivary gland polytene chromosomes of larvae of one of the D. melanogaster strains having a full-length hobo copy.     

Spread of the autonomous transposable element hobo in the genome of Drosophila melanogaster

The transposable element hobo has been introduced into the previously empty Drosophila melanogaster strain Hikone so that its dynamics can be followed and it can be compared with the P element. Five transformed lines were followed over 58 generations. The results were highly dependent on the culture temperature, the spread of hobo element being more efficient at 25 degrees C. The multiplication of hobo sequences resulted in a change in the features of these lines in the hobo system of hybrid dysgenesis. The number of hobo elements remained low (two to seven copies) and the insertions always corresponded to complete sequences. Our findings suggest that, despite their genetic similarities, P and hobo elements differ in many aspects, such as mobility and regulation mechanisms.      

Maintenance of a large pericentric inversion generated by the hobo transposable element in a transgenic line of Drosophila melanogaster

The impact of the hobo transposable element in the global reorganization of the Drosophila melanogaster genome has been investigated in transgenic lines generated by the injection of hobo elements into the Hikone strain, which lacked them previously. Extensive surveys of transgenic lines followed for 250 generations have identified 13 inversions with hobo inserts at most breakpoints. One of these inversions is pericentric on chromosome 2. It has been maintained in the line where it was discovered and in several sublines at frequencies from 0.19 to 0.45, generating stable chromosomal polymorphisms, similar to cosmopolitan paracentric inversions in natural populations. Individuals homozygous for this inversion were viable and fertile, allowing the creation of a new homozygous strain.     

Horizontal transfer of hobo transposable elements within the Drosophila melanogaster species complex: evidence from DNA sequencing.

The hobo family of transposable elements, one of three transposable-element families that cause hybrid dysgenesis in Drosophila melanogaster, appears to be present in all members of the D. melanogaster species complex: D. melanogaster, D. simulans, D. mauritiana, and D. sechellia. Some hobo-hybridizing sequences are also found in the other members of the melanogaster subgroup and in many members of the related montium subgroup. Surveys of older isofemale lines of D. melanogaster suggest that complete hobo elements were absent prior to 50 years ago and that hobo has recently been introduced into the species by horizontal transfer. To test the horizontal transfer hypothesis, the 2.6-kb XhoI fragments of hobo elements from D. melanogaster, D. simulans, and D. mauritiana were cloned and sequenced. The DNA sequences reveal an extremely low level of divergence and support the conclusion that the active hobo element has been horizontally transferred into or among these species in the recent past.     

The effect of gamma-radiation on induction of the hobo element transposition in Drosophila melanogaster

The transposition frequency of the hobo mobile element in four successive generations of Drosophila melanogaster strain y2-717 after an acute gamma-irradiation with a dose of 30 Gr amounted to 7.5 x 10(-4) per site per genome per generation. Under the same conditions, PCR analysis of the genomic DNA of y2-717 flies detected new variants of defective hobo sequence. No changes in the hobo localization and PCR products compared with the control were detected in the case of single irradiation with doses of 3 and 30 Gr. The localizations of hobo element on polytene chromosomes of y2-717 strain did not change during 11 generations after five exposures of flies to 30 Gr. Irradiation of a highly unstable D. melanogaster strain y+743 did not increase the number of families with mutant progeny, yet increased the total number of mutant descendants almost twofold, from 5 to 9%.     

Hoppel-family of mobile elements of Drosophila melanogaster, flanked by short inverted repeats and having preferential localization in the heterochromatin regions of the genome

A mobile element (ME) having 91% homology with Dm1360 (Kholodilov et al., 1987) has been cloned from the Drosophila melanogaster genome and sequenced. The family of ME was designated hoppel. The members of this family are flanked by short inverted repeats likewise P, hobo and HB. The hoppel is hybridized with 10-30 euchromatic sites of polytene chromosomes of different Drosophila stocks. Abundant hybridization with heterochromatic regions of chromosomes-chromocenter, pericentric heterochromatin, the 4 chromosome and telomeres was observed in all stocks of D. melanogaster examined and in D. simulans. At least six genomic variants of ME differing in length of the central part were revealed. Hoppel possesses ARS activity similar to the P element. Two ME hoppel were shown to be arranged as a direct repeat in the recombinant phage.     

Hobo transposons causing chromosomal breakpoints.

Several laboratory surveys have shown that transposable elements (TEs) can cause chromosomal breaks and lead to inversions, as in dysgenic crosses involving P-elements. However, it is not presently clear what causes inversions in natural populations of Drosophila. The only direct molecular studies must be taken as evidence against the involvement of mobile elements. Here, in Drosophila lines transformed with the hobo transposable element, and followed for 100 generations, we show the appearance of five different inversions with hobo inserts at breakpoints. Almost all breakpoints occurred in hobo insertion sites detected in previous generations. Therefore, it can be assumed that such elements are responsible for restructuring genomes in natural populations.     

hobo transposable elements in Drosophila melanogaster and D. simulans.

Genomic patterns of occurrence of the transposable element hobo are polymorphic in the sibling species Drosophila melanogaster and D. simulans. Most tested strains of both species have apparently complete (3.0 kb) and smaller hobo elements (H lines), but in both species some strains completely lack such canonical hobo elements (E lines). The occurrence of H and E lines in D. simulans as well as in D. melanogaster implies that an hypothesis of recent introduction in the latter species is inadequate to explain the phylogenetic occurrence of hobo. Particular internally deleted elements, the approximately 1.5 kb Th1 and Th2 elements, are abundant in many lines of D. melanogaster, and an analogous 1.1 kb internally deleted element, h del sim, is abundant in most lines of D. simulans. Besides the canonical hobo sequences, both species (and their sibling species D. sechellia and D. mauritiana) have many hobo-hybridizing sequences per genome that do not appear to be closely related to the canonical hobo sequence.     

S Elements: A Family of Tc1-like Transposons in the Genome of Drosophila Melanogaster

The S elements form a diverse family of long-inverted-repeat transposons within the genome of Drosophila melanogaster. These elements vary in size and sequence, the longest consisting of 1736 bp with 234-bp inverted terminal repeats. The longest open reading frame in an intact S element could encode a 345-amino acid polypeptide. This polypeptide is homologous to the transposases of the mariner-Tc1 superfamily of transposable elements. S elements are ubiquitous in D. melanogaster populations and also appear to be present in the genomes of two sibling species; however, they seem to be absent from 17 other Drosophila species that were examined. Within D. melanogaster strains, there are, on average, 37.4 cytologically detectable S elements per diploid genome. These elements are scattered throughout the chromosomes, but several sites in both the euchromatin and β heterochromatin are consistently occupied. The discovery of an S-element-insertion mutation and a reversion of this mutation indicates that S elements are at least occasionally mobile in the D. melanogaster genome. These elements seem to insert at an AT dinucleotide within a short palindrome and apparently duplicate that dinucleotide upon insertion.     

Genetic Instability in Drosophila Melanogaster Mediated by Hobo Transposable Elements

Eight independent recessive lethal mutations that occurred on derivatives of an unstable X chromosome (Uc) in Drosophila melanogaster were analyzed by a combination of genetic and molecular techniques. Seven of the mutations were localized to complementation groups in polytene chromosome bands 6E; 7A. In situ hybridization and genomic Southern analysis established that hobo transposable elements were associated with all seven of the mutations. Six mutations involved deletions of DNA, some of which were large enough to be seen cytologically, and in each case, a hobo element was inserted at the junction of the deletion's breakpoints. A seventh mutation was associated with a small inversion between 6F and 7A-B and a hobo element was inserted at one of its breakpoints. One of the mutant chromosomes had an active hobo-mediated instability, manifested by the recurrent production of mutations of the carmine (cm) locus in bands 6E5-6. This instability persisted for many generations in several sublines of an inbred stock. Two levels of instability, high and basal, were distinguished. Sublines with high instability had two hobo elements in the 6E-F region and produced cm mutations by deleting the segment between the two hobos; a single hobo element remained at the junction of the deletion breakpoints. Sublines with low instability had only one hobo element in the 6E-F region, but they also produced deletion mutations of cm. Both types of sublines also acquired hobo-mediated inversions on the X chromosome. Collectively, these results suggest that interactions between hobo elements are responsible for the instability of Uc. It is proposed that interactions between widely separated elements produce gross rearrangements that restructure the chromosome and that interactions between nearby elements cause regional instabilities manifested by the recurrence of specific mutations. These regional instabilities may arise when a copy of hobo transposes a short distance, creating a pair of hobos that can interact to produce small rearrangements.     

Identification of a new hobo element in the cabbage moth, Mamestra brassicae (Lepidoptera)

A complete hobo-like element, called Mbhobo, was identified in the cabbage moth, Mamestra brassicae. This element has a high sequence similarity to the HFL1 hobo element of Drosophila melanogaster. Amplification of Mbhobo termini indicated that transposition occurred into a 5'-GTGGGTAC-3' target sequence that was duplicated upon insertion. This target site conforms to the consensus sequence established for the insertion sites of insect hAT elements. Mbhobo has a single 1935 bp long ORF with significant homology to the D. melanogaster HFL1 hobo transposase. FISH experiments evidenced Mbhobo clusters located in heterochromatic regions of Z and W sex chromosomes and in heterochromatic areas of chromosome pair 10.     

Characterization of hobo element copy number and integrity in Brasilian populations of Drosophila melanogaster

We have determined the copy number and the presence of full-size hobo transposable elements in eight Brasilian strains of Drosophila melanogaster. Genomic DNA was digested with AvaII and XhoI restriction enzymes, respectively, and probed with a 963 bp sequence of the hobo element. Variable numbers of full-sized and defective elements were detected in all strains. The range of the copy number was 22.13 +/- 4.52. Blots showed the presence of a 2.6 kb fragment, corresponding to the complete element, in all strains exception of one and the 1.0 kb sequence, correponding to the Th1 and Th2 repressor elements. There was neither association among copy numbers of hobo elements and latitude nor the mean annual temperatures in the original geographical region of each strain.     

Distribution of hobo transposable elements in the genus Drosophila

This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibling species, D. simulans and D. mauritiana, were found to contain potentially complete hobo elements. The distribution of hobo sequences is one of the narrowest distributions thus far described for any Drosophila transposable element.